Alliance
by John Silver fan
Summary: Palpatine has returned, and this time there's no Vader to stop him. With no other option, the New Republic has allied itself with Grand Admiral Thrawn. Can they prevent the Sith Master from regaining control?
1. Chimaera

**Author's Note: This is my first time writing with Thrawn so please bear with me.**

* * *

><p>There was chaos and panic all around. People were shouting, children and babies crying and screaming for their parents. The very air seemed to taste of fear. There was a great explosion accompanied by dying screams.<p>

Mitth'raw'nuruodo, better known by his core name as Thrawn, sat bolt upright in bed. He looked around, breathing heavily, only to realize he was still in his personal quarters aboard his flagship, the _Chimaera_. He was covered in a cold sweat, and his heart was racing.

It had been thirty-eight years since the destruction of the _Outbound Flight_, and yet his dreams were still occasionally haunted by it. It had been a needless massacre, done mainly to impress Darth Sidious, known better now as Emperor Palpatine.

It still haunted and bothered Thrawn. He had killed _forty-nine thousand, nine hundred and forty-three_ innocent people that day all to try to gain favor of a man he would later come to hate. Yes, he hated the Emperor. The man had promised peace, security, prosperity, and equality. However, the Empire was oppressive, unstable, and, at least in his opinion, unfit as a form of galactic government. People had little freedom of speech about the actual Empire and Emperor himself, the bureaucrats were even more corrupt than they had been during the last days of the Old Republic, the Emperor was a tyrant, and the ruthless Darth Vader commanded the entire Imperial Navy and was the Emperor's second-in-command.

Thrawn shuddered at the thought of Vader. He had met him only a handful of times, but that had been more than enough. He was uncomfortable around the Emperor, but Vader... he felt true fear around Vader. He did, admittedly, respect Vader in some ways. The Dark Lord never gave his men an order himself would not do, he consulted the few he actually seemed to trust, he didn't expect them to be perfect like many other high ranking Imperials did, and he actually fought alongside his men right at the frontline. However, Vader took discipline to the extreme, often killing his own men, though Thrawn had to admit that it was rare that Vader ever killed one of his men simply because he was in a bad mood, though that did make him more _likely_ to kill.

The Chiss shook his head. This was all in the past. Palpatine and Vader were dead. They had been dead for nearly ten years.

Now Thrawn was fighting the New Republic with Darth Vader's own children, Luke Skywalker and Leia Organa Solo, at the helm of the fledging government. Well, he _had_ been fighting them, but an old and common enemy had returned.

Palpatine had returned as a clone.

Leia, knowing that they would need all the help they could get, had proposed an alliance with Thrawn. Neither of them wanted Palpatine back in power, but the New Republic was not fully prepared to face the Sith Master once more. Seeing no other option, they had turned to Thrawn, who understood Palpatine's ways better than anyone else aside from the Emperor himself. They would need a tactical mind like his if they were to be able to defeat Palpatine a second time. The Grand Admiral had agreed, and a reluctant truce was formed.

Sighing, he lay down and went back to sleep.

The next morning, a ship arrived. Thrawn waited in the hangar bay as it landed. The passengers came out, revealing themselves to be Jedi Master Luke Skywalker, Han Solo, and Chewbaca.

"Welcome."

As they walked through the corridors, they made an interesting group. Chewbaca the Wookie with his bowcaster, Han Solo in his pirate clothes, Corellian blood-stripes, a blaster at his belt, brown hair, and brown eyes, Luke Skywalker in his dark Jedi robes, lightsaber at his belt, blond hair, and sky blue eyes, and Thrawn in his white Grand Admiral uniform, black-blue hair, azure skin, and glowing red eyes.

As they stepped into Thrawn's quarters, Luke felt the Force leave.

"What?"

He reached for his lightsaber.

"That won't be necessary, Master Skywalker. There is no danger to you, it's simply my ysalamiri."

Luke then noticed the two furred lizards lounging nearby. He relaxed and slipped his lightsaber back to his belt.

Thrawn sat in his command chair and motioned to the chairs and couch he had had brought in for such an occasion.

"Please, sit."

They sat down, and Thrawn's com beeped.

"Yes?"

"Incoming transmission from Chancellor Solo, sir."

"Send it through."

Moments later a hologram of Leia Organa Solo appeared.

"Chancellor," Thrawn greeted, inclining his head in respect.

"Good day, Admiral. Palpatine has begun attacking ships on their way to and leaving Coruscant, military, civilian, medical, and so on. No ships are safe," Leia said, getting right down to business after the greeting.

Thrawn sat back, steepling his fingers, taking this in.

"He's trying to scare us. He's telling us he's not afraid to attack us."

Leia nodded.

"Yes, that's what we have come up with as well."

"We must show him we won't be so easily intimidated."

The others nodded in agreement.

"But just how are we supposed to do that? We're not ready to attack him directly yet."

The Chiss thought for a moment.

"I'll have to think about it."

"Very well. Luke, Han, and Chewbaca will stay aboard the _Chimaera_ as my representatives. Inform me once you have something, and I shall do the same."

The hologram winked out, and Thrawn activated his comlink.

"Pellaeon, come here please."

"Right away, sir."

A few minutes later the vice admiral entered Thrawn's quarters. He stood an attention and saluted.

"Yes, sir?"

"Master Skywalker, General Solo, and Chewbaca will staying on board as Her Excellency's representatives. Please show them to the civilian deck and give them our finest guest quarters."

Pellaeon nodded.

"Yes, sir. Follow me, please."

Luke, Han, and Chewbaca followed Pellaeon.

A little later, Han and Luke were talking.

"What do you think of Thrawn?"

"He's not evil, if that's what you're asking, Han."

The ex-smuggler looked at his brother-in-law.

"He's just misguided. He believes in the Empire, but..."

"But?"

"But now that he's been working with us and seeing how the New Republic is, he's starting to doubt the Empire."

The older man let this process.

"You think there's hope for him?"

The Jedi nodded.

"If my father could be saved, then I'm sure Thrawn can too."


	2. Insight

**Author's Note:Okay, finally an update.**

* * *

><p>The door com buzzed, and Luke opened it to see a young ensign.<p>

"Master Skywalker?"

"Yes?"

The ensign stood at attention.

"Ensign Drake Hunter. The Grand Admiral wishes to speak with you,... alone."

Luke nodded and followed the young man. Once in Thrawn's quarters he once again felt the affect of the ysalamiri.

"Master Skywalker, thank you for coming," Thrawn said after dismissing Drake.

"Of course, Admiral. How can I help you?"

Thrawn motioned to a chair.

"Please sit, and I will explain why I wished to meet with you alone."

Luke sat down, and Thrawn did the same.

"Now, I know the basics of the Battle of Endor, but rumor has it that you witnessed both the Emperor and Darth Vader's deaths."

Ah, that's why he was here. Thrawn wanted to know what had happened that day.

"It's no rumor, but I must correct you on something."

Thrawn's eyebrows raised.

"Oh?"

"It was Anakin Skywalker who died aboard the Death Star, not Darth Vader."

The Chiss leaned forward some, now truly interested.

"Care to elaborate?"

"Darth Vader was simply the evil of the Emperor that corrupted Anakin Skywalker, he was never his own person. He lived through Anakin. After dueling me in Bespin, Anakin Skywalker began to reawaken. By the time the Battle of Endor rolled around Vader was dying. I guess you could say I killed Darth Vader, but Darth Vader was never intended to have life. My father turned to the Darkside in hopes of saving my mother, but Darth Vader grew quickly through the mass murder of the Jedi and overtook Anakin. The Emperor twisted Darth Vader into the monster you met, but he was never able to completely destroy Anakin Skywalker."

Thrawn steepled his fingers, processing what he had just heard. He knew all too well the affects of the Darkside on a Force Sensitive.

"So you're saying that Darth Vader died before his body?"

"No."

He sat up straight in surprise and confusion.

"No?"

Luke nodded.

"The body was never his. Nothing physical was ever his. It was Anakin Skywalker's. He was born Anakin, he died Anakin, and Vader never had true claim to any of it."

Thrawn's eyebrows were almost to his hairline. Even his brilliant mind could still be baffled by Jedi beliefs and workings.

"Vader was Palpatine's creation, the twisting and corrupting of my father's emotions and soul. Anakin was the galaxy's greatest victim. Vader was nothing more than Palpatine's slave."

"Yet, he killed his Master."

Luke shook his head. He knew Thrawn wanted to understand everything behind the death of the Emperor, and so he would explain it all, no matter how long it took. Understanding that it was Anakin and not Vader would be probably the greatest thing to help Thrawn understand that where he was now, allied with them, was the right place for him to be.

"Anakin killed Palpatine. Vader wanted him dead, yes, but he wanted his place as Emperor and Sith Master. Vader would have waited for Palpatine to exhaust himself killing me before striking. Anakin stopped him from killing me, even while knowing Palpatine's Force Lightning would short circuit his suit and kill him. He did it to save me, not out of revenge or to rise in rank."

The Grand Admiral could feel a slight ache as he tried to process all this.

"I know this is difficult to understand, Admiral, but it's true. Though they shared the same body and mind, Anakin Skywalker and Darth Vader were as different as night and day. Anakin never needed Vader, but Vader could not survive with Anakin. Yes Vader died on the Death Star, but his death wasn't physical."

"One body, two people?"

Luke nodded.

"You make him sound as if he had multiple personalities."

"In a way."

Thrawn sat back.

"I believe I'm beginning to understand what you're saying, Skywalker."

Luke smiled.

_"Most people just think he's crazy."_

The Jedi smiled, but Thrawn looked like he was on the verge of screaming.

"Hello, Father."

Anakin Skywalker's ghost walked into Luke's view.

_"Hello, son. Sorry to scare you, Admiral, but I felt that perhaps seeing me would help cement the concept of what Luke told you."_

Thrawn stared at the ghost. He was young, tall, and handsome, not at all what he had pictured to be behind the mask of Darth Vader.

Anakin smiled, sensing Thrawn's thoughts.

_"This isn't what I looked like behind that mask."_

Suddenly the image changed to a scarred man with not a single hair upon his head. Thrawn had seen corpses that looked better that he did.

_"**This** is what I looked like behind the mask."_

The Chiss swallowed, and Anakin turned back to normal.

"What... what happened to you?"

An old man dressed like Anakin appeared beside him.

_"I'm afraid I am to blame for his appearance and the need for that suit."_

"Hello, Ben."

Obi-Wan 'Ben' Kenobi smiled at Luke.

_"After Anakin killed the Separatists on Mustafar, his wife and I found him there. Blinded by his anger, he choked her, accusing her of bringing me there to kill him. We fought, and I cut off his left arm and both legs."_

_"I slid down the bank and ended up catching on fire."_

Thrawn turned pale and winced at the thought.

_"The fire damaged my lungs, eyes, and destroyed my hearing. Without that suit, I could not breathe on my own, see as well as I needed to, and I could not hear at all without the mask. You saw me as the pinnacle of strength, but in reality I was a broken man who depended on machinery just to breathe."_

"So when he grabbed Palpatine and threw him down to the reactor core, the lightning fired the life support system of the suit," Luke said.

The Grand Admiral looked at Luke then back at the ghosts.

_"Yes, so before Luke ever removed my mask, my fate was sealed. Removing the mask simply brought it on quicker."_

"Then why did you have him remove the mask?"

Anakin smiled sadly.

_"Though the mask helped me see, my vision was forever tinted red by it. I wanted to see my son as he truly was, with my own eyes, before I died. Thrawn, I know you feared me as Vader, and it's time to stop fighting for what he wanted, it's time to stop fighting for the Empire. In doing so, you keep the beliefs of Palpatine and Vader alive."_

The ghosts disappeared.

Thrawn dismissed Luke and sat thinking about what all he had learned and been told.

* * *

><p><strong>End Note: Anakin and Obi-Wan make an appearance, and Thrawn gets insight into Vader and Anakin.<strong>


	3. Naming

**Author's Note: At last an update! Sorry, guys, my computer crashed, and I lost everything. I finally got the inspiration and motivation to update this one.**

* * *

><p>Thrawn sat in his command chair after Luke left, thinking over what he had just heard.<p>

Was it really time to give up on the Empire?

One of his ysalamir broke his thoughts by chasing the other... all over him. Sputtering in surprise, he quickly tried to catch one of them. The smaller lizard, the one being chased, leaped off the arm of the chase to dash across the room. The bigger one instantly gave chase. Thrawn sighed and followed, knowing the bigger one, a male, could get rough when wanting to play like this.

A squeal was heard, and his little female came rushing towards him, sporting a bite on her front left leg. The Grand Admiral quickly scooped her and sidestepped the overenthusiastic male, who tried to climb up his master to reach his playmate. The Chiss was once again reminded that they were still very playful animals, especially since they seemed to know that they were in no danger aboard the _Chimera._

Vice Admiral Pellaeon came in to see his commander grappling with his pets, trying to keep the little female from being bullied by the male, while the male, in his eagerness to play, clambered all over Thrawn. For a moment all he could do was stare until Thrawn spotted him.

"Well don't just stand there, grab him!"

"Yes, sir!"

Pellaeon hurried over and caught the furred lizard, who struggled in his grip.

"At it again are they?"

Thrawn sighed in exasperation.

"Yes."

He stroked the female in his arms and let her climb onto his shoulders to dig her claws into the nutrient frame he wore under his clothes so the ysalamir wouldn't go hungry when on his back. Pelleaon wore one as well and was allowing the male up onto his shoulders now as well.

"Would you take him with you for a while until he calms down?"

"Of course, sir."

Thrawn then remembered that Pellaeon had come in here for a reason.

"Did you need something?"

"Oh. Yes. Master Skywalker has asked if there is a place for him to practice with his lightsaber. I thought it best to check with you first."

Thrawn nodded.

"I'll show him. Dismissed."

Pellaeon saluted and left with the male ysalamir. Thrawn looked at the female, who cocked her head at him. Of the two lizards she was the most attached to him.

"Well, my sweet one, shall we go show the Jedi where to practice?"

She licked his cheek, and he walked off, chuckling.

Luke opened the door when it buzzed. Having felt the effects of the ysalamir, he wasn't surprised to see Thrawn on the other side.

"Admiral."

"I was told you wished to practice with your lightsaber. There is a private training room I occasionally use that should suit your needs."

Luke smiled.

"Thank you."

"If you'll come with me, I'll show you where."

The Jedi followed Thrawn through the ship. The little female looked at the newcomer curiously. Luke looked back.

"Having a staring contest with my lizard, Master Skywalker?" Thrawn drawled.

Luke blushed and chuckled.

"Sorry. Uh, what's her name?"

"Name?"

He nodded.

"Yeah. Her name."

Thrawn gave him a blank look.

"You didn't name them?"

"No. I guess it never occurred to me to do so."

Luke turned his attention back to the ysalamir, studying her. She stared back as he leaned in a little closer, aware of Thrawn watching him curiously. The little female chirped and licked his face.

"Ah! Bleh!"

Thrawn chuckled.

"I suppose I should have warned you about that. She's very affectionate."

Luke wiped off his face.

"I noticed, and I have the perfect name for her."

"Oh?"

"Esti."

Thrawn blinked.

"Esti?"

"Yeah. It means 'sweet' or 'honey'."

The Chiss looked at his pet.

"What do you think?"

She lightly butted his face.

"I'll take that as a yes. Esti it is."

The newly christened Esti contented herself with nibbling at Thrawn's hair. They finally arrived at the training room, and Thrawn showed Luke the combination to unlock it.

"Thank you, Admiral."

"You're welcome."

Thrawn left Luke alone to train, heading back to his rooms.

* * *

><p><strong>End Note: So one ysalamir has been named. Thrawn has a choice to make soon. Republic or Empire? What will he choose? Palpatine is lurking out there somewhere, I just have to find him, though I don't really want to. Please review.<strong>


	4. Thrawn's Choice

**Author's Note: Another update. I don't know how Thrawn actually treats his ysalamir, but I want to show him as a fairly good owner than cares about his pets.**

* * *

><p>Luke named the male Kerr, which meant 'man of strength'. He noticed strange stands all over the Chimaera. Thrawn explained that these were nutrient stands so the lizards would have full reign of the ship rather than being dependent on him and Pallaeon. He, Han, and Chewbaca had some trouble telling to the two lizards apart, while the residents of the Star Destroyer easily knew which lizard was which. Kerr wasn't actually that much bigger than Esti.<p>

"Why don't you just put colored collars on them?" Han asked Thrawn as they walked to the bridge.

Thrawn gave Esti, who was sleeping on his shoulders, a thoughtful stroke.

"We tried that at first."

Chewbaca moaned, asking what happened, and Thrawn was glad he understood Shriiwook so there was no translation needed.

"Pallaeon and I know how chew toys feel."

They reached the bridge, and as if in respond to Thrawn's comment, Kerr was making a nuisance out of himself by chewing on Pallaeon's cap, while it was still on the Vice-Admiral's head.

"Why do they have teeth if they draw nutrients from trees, or in this case the frames and stands, through their claws?"

"Most likely for defense," Pallaeon answered, reaching up to lightly smack Kerr on the nose when the lizard pulled his hair trying to get the cap off.

Kerr blinked then climbed down with a grumbling noise. Luke chuckled.

"Guess he didn't appreciate that."

"Well, Master Skywalker, I don't really appreciate him giving me a bald spot just because he wants my cap."

Kerr butted Luke's leg, and the Jedi bent to pet him. From what he had seen ysalamir were very intelligent. They recognized people, certain commands, their new names, and when someone was new. They were very playful and friendly.

Kerr was the one to most often stray from Thrawn to roam the ship, getting attention from the crew members. Esti was rarely seen very far from the Grand Admiral, his shoulders being her favorite place. Though he often strayed from his master, Kerr obviously loved Thrawn as much as any pet could love their owner, just as Esti did. If Esti occupied the Chiss's shoulders, Kerr was either in his arms or trotting alongside him. Both were also obviously fond of Pallaeon, who often had one of them, usually Kerr, across his shoulders or at his side.

Luke had noticed one thing that bothered him. The ysalamir were very friendly to everyone aboard except for one individual; Thrawn's Noghri bodyguard, Rukh. They hissed and growled at him almost every time they saw him.

"Hardly anyone here likes Rukh," Thrawn said when Luke questioned him about it.

The Jedi decided to let it go for now.

One day, Thrawn was sitting in his command chair. Kerr was on his shoulders while Esti was in his lap, enjoying being petted. He had long since learned to sense Rukh's presence near him, so he wasn't surprised when the Noghri came up behind him. He _was,_ however, surprised, when both ysalamir suddenly launched themselves at his bodyguard just as Pallaeon came on.

"Sir!" Pallaeon shouted over Rukh's startled cries of pain.

Thrawn shot up and whirled around to see Kerr and Esti biting down on Rukh's wrist, clawing at him. An instant later he discovered why his usually peaceful pets were attacking Rukh. His knife was in his hand, and Thrawn put it all together in seconds. The assassin had been about to kill him.

Pallaeon came up to the Grand Admiral, staring at the Noghri and ysalamir in shock. Both Imperials were forzen in stunned silence until Rukh managed to fling the lizards to the floor, knife now turned on them.

"No!" Thrawn cried, lunging forward.

Rukh was unprepared for the attack, and the taller, heavier Chiss took him down. They wrestled for the knife, while Pallaeon called for help. Luke, Han, and Chewbaca arrived first as Luke had sensed danger.

A crack and cry of pain alerted them to the fact that Thrawn had managed to break Rukh's wrist, making him drop the knife. The assassin raked his claws across Thrawn's face, seeking to take out of his eyes. He threw the Chiss off only to find himself under the point of Luke's lightsaber.

"Are you all right, Admiral?"

"I will be once I put some bacta on these cuts. Rukh, why are you trying to kill me?"

"The Empire betrayed us! You would have us as slaves!"

"We're not the Empire anymore, Rukh. I have no interest in forcing you or your people to do anything you don't want to."

Rukh growled.

"I don't believe you. I'll kill you if it's the last thing I do."

Thrawn sighed.

"Then you must die."

"What?!" Luke exclaimed.

"He won't stop until one of us is dead. I don't _want_ to kill him, but it must be done."

Pallaeon drew his blaster and fired once, killing Rukh.

"Sir, you said we're not the Empire anymore."

Luke and Han exchanged smiled.

"Yes, Pallaeon. Palpatine means to kill us all. We will join the Republic."

Pallaeon blinked then nodded.

"Yes, sir."

* * *

><p><strong>End Note: Thrawn has made his choice. Please review.<strong>


End file.
